Contacts of the strand formed by residues 95 - 106 (chain G) in PDB entry 1FSK
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with LEU 95 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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90G PRO* 3.2 35.2 - - + +
91G ILE* 3.9 3.0 - - + +
92G GLY* 2.8 31.3 + - - -
93G ASP 4.0 2.6 + - - +
94G THR* 1.3 84.7 + - - +
96G GLU* 1.3 64.2 + - - +
97G LYS 3.9 13.9 - - - +
98G ILE* 3.5 31.0 - - + -
120G TYR* 3.6 25.1 - - + -
121G HIS 3.0 37.7 - - - +
122G THR* 4.4 5.2 - - + -
132G GLN* 5.5 2.2 - - + -
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Residues in contact with GLU 96 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86G ILE 4.5 3.3 - - - +
91G ILE* 3.1 23.5 - - - +
95G LEU* 1.3 72.8 - - - +
97G LYS* 1.3 66.9 + - + +
121G HIS* 2.8 30.2 + - + +
122G THR 4.3 11.0 - - - +
123G LYS* 3.2 40.7 + - + -
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Residues in contact with LYS 97 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70G ARG* 3.8 12.9 - - - +
84G SER* 3.8 13.8 + - - -
85G VAL 3.4 14.8 - - - +
86G ILE* 4.6 10.5 - - + -
91G ILE* 3.6 4.0 - - - -
95G LEU* 3.9 1.3 - - - +
96G GLU* 1.3 85.2 - - + +
98G ILE* 1.3 65.7 - - - +
99G SER* 3.6 19.0 + - - -
121G HIS* 3.0 50.0 + - + +
55I ASP* 3.5 39.0 + - + +
57I TYR* 5.3 1.6 - - - -
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Residues in contact with ILE 98 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84G SER* 3.2 6.4 - - - -
85G VAL* 2.8 50.3 + - + -
90G PRO* 3.8 22.9 - - + -
91G ILE* 4.1 3.6 - - + -
95G LEU* 3.5 31.6 - - + -
97G LYS* 1.3 76.5 - - - +
99G SER* 1.3 63.2 + - - +
100G ASN* 3.1 24.5 + - - +
118G ASN* 4.3 2.5 - - - +
119G LYS 3.5 8.7 - - - +
120G TYR* 3.9 34.1 - - + -
132G GLN* 5.5 0.9 - - - +
136G SER* 5.8 1.6 - - - +
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Residues in contact with SER 99 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83G TYR 3.7 5.6 - - - -
84G SER* 4.3 6.1 - - - -
97G LYS* 3.6 14.9 + - - -
98G ILE* 1.3 70.9 - - - +
100G ASN* 1.3 71.2 + - - +
118G ASN* 3.5 0.5 - - - -
119G LYS* 3.0 48.0 + - - -
121G HIS* 2.8 27.8 - - - -
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Residues in contact with ASN 100 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82G ASN* 3.3 7.0 - - - +
83G TYR* 2.8 81.2 + - + +
85G VAL* 3.7 12.7 - - - +
98G ILE* 3.1 20.7 + - - +
99G SER* 1.3 89.0 - - - +
101G GLU* 1.3 62.8 + - - +
102G ILE* 5.5 1.8 - - + -
116G ILE* 5.9 1.1 - - + -
117G SER 3.9 7.0 - - - +
118G ASN* 3.0 23.0 - - - +
119G LYS* 3.3 6.3 + - - +
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Residues in contact with GLU 101 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80G LYS* 2.9 43.7 + - + +
81G TYR 3.6 4.0 - - - -
82G ASN* 3.1 23.7 + - - +
100G ASN* 1.3 78.5 - - - +
102G ILE* 1.3 67.5 + - - +
103G LYS* 4.2 9.0 + - + +
115G LYS 3.7 1.0 - - - +
116G ILE* 3.3 6.8 - - - +
117G SER* 3.0 37.1 + - - +
119G LYS* 3.7 10.6 + - - +
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Residues in contact with ILE 102 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19G PHE* 5.4 0.3 - - - -
22G PHE* 4.8 9.6 - - + -
23G ILE* 4.3 25.8 - - + -
79G PHE 3.5 4.5 - - - +
80G LYS* 3.5 0.3 - - - -
81G TYR* 2.9 43.8 + - + +
83G TYR* 4.2 24.5 - - + +
100G ASN* 5.5 0.9 - - + -
101G GLU* 1.3 81.2 - - - +
103G LYS* 1.3 66.2 + - - +
104G ILE* 4.5 14.8 - - + -
114G LEU* 4.9 8.3 - - + -
115G LYS 3.5 9.0 - - - +
116G ILE* 4.0 26.7 - - + -
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Residues in contact with LYS 103 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78G ASN* 3.2 31.3 + - - +
79G PHE 3.6 2.7 - - - -
80G LYS* 4.3 20.9 - - + +
101G GLU* 4.2 11.4 - - - +
102G ILE* 1.3 75.3 - - - +
104G ILE* 1.3 82.1 + - - +
105G VAL* 3.7 28.8 - - + +
113G ILE 3.6 0.9 - - - +
114G LEU* 3.5 4.9 - - - +
115G LYS* 3.0 48.4 + - + +
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Residues in contact with ILE 104 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15G ALA* 3.3 33.7 - - + +
18G LEU* 4.0 24.0 - - + +
19G PHE* 4.0 28.9 - - + -
22G PHE* 5.0 2.2 - - + -
23G ILE* 4.6 9.9 - - + -
79G PHE* 3.3 40.5 + - + +
102G ILE* 4.5 7.9 - - + -
103G LYS* 1.3 89.9 - - - +
105G VAL* 1.3 60.9 + - - +
112G SER* 4.2 9.0 - - - +
113G ILE 3.3 6.5 - - - +
114G LEU* 4.0 18.8 - - + -
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Residues in contact with VAL 105 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15G ALA* 3.9 3.8 - - - -
103G LYS* 3.7 31.0 - - + +
104G ILE* 1.3 72.3 - - - +
106G ALA* 1.3 62.7 + - - +
107G THR* 3.4 0.7 + - + -
112G SER* 3.2 4.9 - - - -
113G ILE* 2.9 68.2 + - + +
115G LYS* 4.3 26.2 - - + +
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Residues in contact with ALA 106 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14G PRO* 5.7 1.3 - - + -
15G ALA* 3.7 21.4 - - + +
16G ALA 5.5 0.2 - - - +
79G PHE* 5.8 2.9 - - + -
105G VAL* 1.3 71.3 - - - +
107G THR* 1.3 64.9 + - - +
108G PRO* 3.9 2.1 - - - +
110G GLY 5.3 2.0 - - - +
111G GLY 3.8 10.5 - - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il